DDX28

DEAD-box helicase 28, the group of DEAD-box helicases

Basic information

Region (hg38): 16:68020916-68023232

Links

ENSG00000182810 ∙ NCBI:55794 ∙ OMIM:607618 ∙ HGNC:17330 ∙ Uniprot:Q9NUL7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DDX28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX28 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in DDX28

This is a list of pathogenic ClinVar variants found in the DDX28 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-68021658-A-C		not specified	Uncertain significance (Feb 07, 2023)
16-68021698-A-G		not specified	Uncertain significance (Jul 27, 2022)
16-68021782-A-G		not specified	Uncertain significance (Jul 07, 2024)
16-68021788-T-C		not specified	Uncertain significance (Jul 26, 2021)
16-68021930-G-C		not specified	Uncertain significance (Nov 15, 2024)
16-68022041-G-A		not specified	Uncertain significance (Nov 20, 2024)
16-68022062-G-T		not specified	Uncertain significance (Mar 06, 2023)
16-68022067-G-A		not specified	Uncertain significance (Oct 05, 2023)
16-68022187-T-A		not specified	Uncertain significance (Nov 14, 2023)
16-68022235-T-A		not specified	Uncertain significance (Feb 16, 2023)
16-68022311-C-G		not specified	Uncertain significance (Aug 08, 2022)
16-68022326-C-T		not specified	Uncertain significance (Nov 09, 2023)
16-68022358-A-G		not specified	Uncertain significance (Jan 24, 2023)
16-68022472-C-A		not specified	Uncertain significance (Feb 06, 2023)
16-68022513-C-G		not specified	Uncertain significance (Apr 20, 2023)
16-68022557-C-G		not specified	Uncertain significance (Oct 13, 2023)
16-68022566-G-C		not specified	Uncertain significance (Feb 16, 2023)
16-68022667-G-A		not specified	Uncertain significance (Nov 30, 2021)
16-68022707-G-A		not specified	Uncertain significance (Aug 02, 2021)
16-68022724-G-A		not specified	Uncertain significance (Sep 11, 2024)
16-68022739-T-C		not specified	Uncertain significance (Dec 06, 2022)
16-68022749-T-C		not specified	Uncertain significance (Oct 07, 2024)
16-68022809-C-A		not specified	Uncertain significance (Jun 07, 2023)
16-68022826-C-T		not specified	Uncertain significance (Sep 03, 2024)
16-68022886-T-C		not specified	Uncertain significance (Nov 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX28	protein_coding	protein_coding	ENST00000332395	1	2592

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-8	0.206	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.747	337	301	1.12	0.0000150	3367
Missense in Polyphen		98	90.336	1.0848		1120
Synonymous	-0.437	145	138	1.05	0.00000688	1268
Loss of Function	0.388	13	14.6	0.890	7.71e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function (PubMed:25683708, PubMed:25683715). May be involved in RNA processing or transport. Has RNA and Mg(2+)-dependent ATPase activity (PubMed:11350955). {ECO:0000269|PubMed:11350955, ECO:0000269|PubMed:25683708, ECO:0000269|PubMed:25683715}.

Recessive Scores

• pRec: 0.0840

Intolerance Scores

• loftool: 0.601
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.0753
• hipred: Y
• hipred_score: 0.563
• ghis: 0.396

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ddx28

Gene ontology

• Biological process: mitochondrial large ribosomal subunit assembly
• Cellular component: nucleus;nucleolus;mitochondrion;cytosol;ribonucleoprotein granule;mitochondrial nucleoid
• Molecular function: RNA binding;helicase activity;ATP binding;rRNA binding